I asked this question a few days ago on reddit. Your LORs need to be submitted to the schools before your secondary is marked complete. Until then they won't look at it. You can submit your secondary, then once your letters come in it will be reviewed. At least that's the impression that I got. It should be noted that some schools require you to submit your secondary within a month of it becoming available to you, like OHSU and U of Utah. If your letters aren't in within that month, your app will be tossed out and your secondary fee is essentially a donation to the school. I don't think most schools are like this but definitely take a look before you submit your primary.